The findings are published today by the Children's Rights Alliance for England (CRAE), which accuses policymakers of allowing progress on a number of young people's rights to drift "backwards" while they focus on Brexit.
The areas of concern flagged by The State of Children's Rights in 2018 report, span housing, policing, education and mental health.
The report highlights how the UK's decision to leave the European Union has dominated the political debate at a time when the number of children living in relative poverty in the UK (after housing costs) increased to 4.1 million in 2016/17, "making it difficult to secure attention for issues affecting children".
The report provides fresh analysis of children's legal position and new freedom of information (FOI) data.
According to the responses from 58 per cent of 353 councils approached, in 2017, almost two thirds of families with children who were housed in council-owned bed and breakfast accommodation, remained there for longer than six weeks.
This equated to 1,056 of the 1,641 families in council-owned B&Bs and hotel-style accommodation. "The real number is likely to be much higher," the report states.
Six weeks is the maximum time councils are allowed to house families in private B&Bs, but this limit does not apply to council-owned accommodation.
However, CRAE, which is the policy arm of children's charity Just for Kids Law, suggested council practice ignores the spirit of the legislation.
The UK government is a signatory to the UN Convention on the Rights of the Child, which sets a six-week legal limit on temporary housing, and stipulates that every child has the right to grow up in a healthy environment.
The CRAE report claims that B&B accommodation is "completely unsuitable for children".
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"Very young children have nowhere to play, crawl and learn to walk, and parents often struggle to set up regular sleep routines or potty train, while older children have no privacy and have nowhere to study or socialise with friends," it states.
CRAE also asked councils about numbers of looked-after children in independent accommodation, which included unsupervised B&Bs.
The results provided by the quarter of authorities that responded showed at least 1,173 had been placed in such lodgings for more than six months, including 19 children aged 15 and one aged 14.
Police are also increasingly using dangerous intervention, according to FOI responses from 29 of the 39 police forces approached.
Electric stun guns were used on children 871 times in 2017, while between January and September 2018 the figure was 839.
Tasers were also used disproportionately against children from BAME backgrounds, at 51 per cent of taser use.
A further 23 police forces confirmed using spit-hoods on children 47 times in 2017, and at least 114 times in the first nine months of 2018.
Louise King, director of CRAE and policy and campaigns at Just for Kids Law, said the country had "sadly taken steps backwards in many areas".
"It is essential that government and parliamentarians focus attention and resources on addressing the issues outlined in this report and put the safety and wellbeing of children at the centre of policy decisions," she added.
Children's Rights Alliance for England campaign video on children living in B&B accommodation